From a383b8432db05235210e23873db1a257a4a73fab Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 3 Oct 2014 12:02:09 +0100
Subject: [PATCH] JAL-1481 search expression validation

---
 src/jalview/gui/Finder.java |  110 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 87 insertions(+), 23 deletions(-)

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index bc5f823..8eddc06 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -20,23 +20,38 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.event.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
 
-import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
 
 /**
- * DOCUMENT ME!
+ * Performs the menu option for searching the alignment, for the next or all
+ * matches. If matches are found, they are highlighted, and the user has the
+ * option to create a new feature on the alignment for the matched positions.
+ * 
+ * Searches can be for a simple base sequence, or may use a regular expression.
+ * Any gaps are ignored.
  * 
  * @author $author$
  * @version $Revision$
  */
 public class Finder extends GFinder
 {
+  private static final int HEIGHT = 110;
+
+  private static final int WIDTH = 340;
+
   AlignViewport av;
 
   AlignmentPanel ap;
@@ -50,14 +65,7 @@ public class Finder extends GFinder
   SearchResults searchResults;
 
   /**
-   * Creates a new Finder object.
-   * 
-   * @param av
-   *          DOCUMENT ME!
-   * @param ap
-   *          DOCUMENT ME!
-   * @param f
-   *          DOCUMENT ME!
+   * Creates a new Finder object with no associated viewport or panel.
    */
   public Finder()
   {
@@ -65,6 +73,13 @@ public class Finder extends GFinder
     focusfixed = false;
   }
 
+  /**
+   * Constructor given an associated viewport and alignment panel. Constructs
+   * and displays an internal frame where the user can enter a search string.
+   * 
+   * @param viewport
+   * @param alignPanel
+   */
   public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
   {
     av = viewport;
@@ -73,16 +88,16 @@ public class Finder extends GFinder
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+            WIDTH, HEIGHT);
 
     textfield.requestFocus();
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find Next' action.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   public void findNext_actionPerformed(ActionEvent e)
   {
@@ -93,10 +108,9 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find All' action.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   public void findAll_actionPerformed(ActionEvent e)
   {
@@ -178,10 +192,10 @@ public class Finder extends GFinder
   }
 
   /**
-   * incrementally search the alignment
+   * Search the alignment for the next or all matches. If 'all matches', a
+   * dialog is shown with the number of sequence ids and subsequences matched.
    * 
    * @param findAll
-   *          true means find all results and raise a dialog box
    */
   void doSearch(boolean findAll)
   {
@@ -189,7 +203,7 @@ public class Finder extends GFinder
 
     String searchString = textfield.getText().trim();
 
-    if (searchString.length() < 1)
+    if (isInvalidSearchString(searchString))
     {
       return;
     }
@@ -269,4 +283,54 @@ public class Finder extends GFinder
     }
 
   }
+
+  /**
+   * Displays an error dialog, and answers false, if the search string is
+   * invalid, else answers true.
+   * 
+   * @param searchString
+   * @return
+   */
+  protected boolean isInvalidSearchString(String searchString)
+  {
+    String error = getSearchValidationError(searchString);
+    if (error == null)
+    {
+      return false;
+    }
+    JOptionPane.showInternalMessageDialog(this, error,
+            MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+            JOptionPane.ERROR_MESSAGE);
+    return true;
+  }
+
+  /**
+   * Returns an error message string if the search string is invalid, else
+   * returns null.
+   * 
+   * Currently validation is limited to checking the string is not empty, and is
+   * a valid regular expression (simple searches for base sub-sequences will
+   * pass this test). Additional validations may be added in future if the
+   * search syntax is expanded.
+   * 
+   * @param searchString
+   * @return
+   */
+  protected String getSearchValidationError(String searchString)
+  {
+    String error = null;
+    if (searchString == null || searchString.length() == 0)
+    {
+      error = MessageManager.getString("label.invalid_search");
+    }
+    try
+    {
+      Pattern.compile(searchString);
+    } catch (PatternSyntaxException e)
+    {
+      error = MessageManager.getString("error.invalid_regex") + ": "
+              + e.getDescription();
+    }
+    return error;
+  }
 }
-- 
1.7.10.2